Tree cavities are used as shelter and breeding nests by numerous avian and mammalian species. In cold environments, tree cavities are often proposed as the best winter nest choice because of the superior protection they offer from precipitation, wind, cold temperatures, and predators. As such, they represent a critical resource, which has the potential to limit population size of non-excavating species. We assessed factors affecting site occupancy in the boreal forest by northern flying squirrels, a secondary user of tree cavities, and to identify which nest type is preferred during the colder days of the autumn—winter period. We trapped flying squirrels twice in 59 aspen-dominated stands in the autumn period using low- (1.5 m above ground-level) and high-mounted (4 m) traps to determine site occupancy. A total of 85 individuals were captured on 2,880 trap-nights. During the winter period, we radio-tracked 26 individuals to 87 diurnal nests in 220 locations. None of the habitat variables considered (cavity availability, woody debris, and lateral cover) explained site occupancy. Detectability decreased with precipitation, and was lower using high traps than low traps. Both females and males used tree cavities (26%), external nests (39%), and ground nests (35%). In cold weather, females preferred ground nests, whereas males preferred external nests. Our results do not support the hypothesis that tree cavities represent a limiting factor to northern flying squirrels in cold environments. Instead, this species seems to be a generalist and is opportunistic, using a variety of nest types. Nevertheless, practices ensuring the persistence of large diameter live cavity trees, providing better insulative properties, are likely to increase the relative use of tree cavities as nest sites by northern flying squirrels.